make_fragment

[Grace Hopper]

i got this massage once try to run make_fragment.pl

[hasni@localhost frag_phad]$ ./make_fragments.pl -verbose -nohoms
-nojufo -nosam phad_.fasta > phad.log
Warning: can’t find executable file /home/hasni/fragment/jufo/molecule.exe!
Warning: can’t find executable file
/home/hasni/fragment/sam3.5.i686-linux/bin/target99!
Warning: can’t find executable file
/home/hasni/fragment/sam3.5.i686-linux/bin/uniqueseq!
Warning: can’t find executable file /home/hasni/fragment/sam.predict-2nd/!
Warning: can’t find executable file
/home/hasni/fragment/sam.predict-2nd/predict-2nd!
/home/hasni/fragment/rosetta_fragments/nnmake/run_prof.py:139:
SyntaxWarning: local name ‘seq’ in ‘Make_full_alignment’ shadows use of
‘seq’ as global in nested scope ‘lambda’
def Make_full_alignment( fasta_seq, align2query, full_seq ):
psiblast_file= ss_blast round: 1 nseq: 76 max_e: 0.001
psiblast_file= ss_blast round: 2 nseq: 419 max_e: 0.001
Traceback (most recent call last):
File “/home/hasni/fragment/rosetta_fragments/nnmake/run_prof.py”, line
246, in ?
align2query, full_seq = Read_psiblast( fasta_seq, psiblast_file,
EVALUE_THRESHOLD )
File “/home/hasni/fragment/rosetta_fragments/nnmake/run_prof.py”, line
70, in Read_psiblast
assert l[5] == ‘Expect’
IndexError: list index out of range
/home/hasni/fragment/rosetta_fragments/nnmake/run_prof.py:139:
SyntaxWarning: local name ‘seq’ in ‘Make_full_alignment’ shadows use of
‘seq’ as global in nested scope ‘lambda’
def Make_full_alignment( fasta_seq, align2query, full_seq ):
psiblast_file= ss_blast round: 1 nseq: 76 max_e: 0.001
psiblast_file= ss_blast round: 2 nseq: 419 max_e: 0.001
Traceback (most recent call last):
File “/home/hasni/fragment/rosetta_fragments/nnmake/run_prof.py”, line
246, in ?
align2query, full_seq = Read_psiblast( fasta_seq, psiblast_file,
EVALUE_THRESHOLD )
File “/home/hasni/fragment/rosetta_fragments/nnmake/run_prof.py”, line
70, in Read_psiblast
assert l[5] == ‘Expect’
IndexError: list index out of range
prof failed.
[hasni@localhost frag_phad]$

what’s wrong ?

[Anonymous]

Hi,
it looks that you did not install the requied software such as JuFo .

[Grace Hopper]

where can i download jufo?
i went to the http://www.meilerlab.org/ but nothing i can download

[Joanna Slusky]

The same problem. Can’t find where to download jufo and sam programs.
(:cry:)

[Sally Ride]

Hi,

I do not have those programs installed also. The very good solution is to run without them:
^make_fragments.pl -nosam -nojufo -noprof -verbose prefix_.fasta^
which requires only easy to get psipred.

Then get SS predictions from any server or metaserver (I use of course GeneSilico MetaServer which gives SS preds from many different programs as well as simple consensus prediction).

Edit 4-letter prefix_.psipred if You think that this secondary structure prediction is not correct,, carefully change the predicted secondary structure states as well as a confidence levels based on the external server results.

You have to generate fragments again: First delete files looking like this:
aaXXXX_03_05.200_v1_3 (3 aa fragments)
aaXXXX_09_05.200_v1_3 (9 aa fragments)
XXXX_.psipred_ss2 (ss in different format)

Than run
^pNNMAKE.gnu aa 4-letter prefix _^

This is potentially very good approach as you have total control on your starting SS preds, you can use many more external SS servers, and you do not need to install them locally.

> The same problem. Can’t find where to download jufo and sam programs.
> (:cry:)

[Anonymous]

Yes, Kosa is right that you can use -nojufo -nosam flag to get fragments generated without them. Robetta server was done due to limited resources. We will set up an other computer to run fragment server asap.

> Hi,
>
> I do not have those programs installed also. The very good solution is to run without them:
> ^make_fragments.pl -nosam -nojufo -noprof -verbose prefix_.fasta^
> which requires only easy to get psipred.
>
> Then get SS predictions from any server or metaserver (I use of course GeneSilico MetaServer which gives SS preds from many different programs as well as simple consensus prediction).
>
> Edit 4-letter prefix_.psipred if You think that this secondary structure prediction is not correct,, carefully change the predicted secondary structure states as well as a confidence levels based on the external server results.
>
> You have to generate fragments again: First delete files looking like this:
> aaXXXX_03_05.200_v1_3 (3 aa fragments)
> aaXXXX_09_05.200_v1_3 (9 aa fragments)
> XXXX_.psipred_ss2 (ss in different format)
>
> Than run
> ^pNNMAKE.gnu aa 4-letter prefix _^
>
> This is potentially very good approach as you have total control on your starting SS preds, you can use many more external SS servers, and you do not need to install them locally.
>
> > The same problem. Can’t find where to download jufo and sam programs.
> > (:cry:)

[malmstroem]

Does anyone know where to get SAM’s predict-2nd program for use with make_fragments.pl? I can’t find it in the most recent releases of [http://www.soe.ucsc.edu/research/compbio/sam2src|SAM]. Thanks.

[Grace Hopper]

ok thanks,
its work

hasni

[Author]

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